I had an issue similar to this but I think you probably already tried what eventually fixed it for me.
My issue had to do with a guild faction change. I had changed the GM for the guild but had not logged in the character that was made the new GM. Once I logged in the character that was the new GM, voila! Guild was transferred.
Not sure that will work for your troubles, but if you haven't already done that, you might give it a whirl.
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